Publications

Provable Sample-Efficient Transfer Learning Conditional Diffusion Models via Representation Learning
Ziheng Cheng, Tianyu Xie, Shiyue Zhang, Cheng Zhang.
Preprint, arXiv:2502.04491, 2025
[Paper]

PhyloVAE: Unsupervised Learning of Phylogenetic Trees via Variational Autoencoders
Tianyu Xie, Harry Richman, Jiansi Gao, Frederick A Matsen IV, Cheng Zhang.
International Conference on Learning Representations (ICLR), 2025
[Paper] [Code]

Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions
Tianyu Xie, Frederick A Matsen IV, Marc A Suchard, Cheng Zhang.
Preprint, arXiv:2408.05058, 2024
[Paper] [Code]

Improving Tree Probability Estimation with Stochastic Optimization and Variance Reduction
Tianyu Xie$^\ast$, Musu Yuan$^\ast$, Minghua Deng, Cheng Zhang.
Statistics and Computing, 34(186), 2024
[Paper] [Code]

Reflected Flow Matching
Tianyu Xie$^\ast$, Yu Zhu$^\ast$, Longlin Yu$^\ast$, Tong Yang, Ziheng Cheng, Shiyue Zhang, Xiangyu Zhang, Cheng Zhang.
International Conference on Machine Learning (ICML), 2024
[Paper] [Code]

Kernel Semi-Implicit Variational Inference
Ziheng Cheng$^\ast$, Longlin Yu$^\ast$, Tianyu Xie, Shiyue Zhang, Cheng Zhang.
International Conference on Machine Learning (ICML), 2024
[Paper] [Code]

Diffusion-PINN Sampler
Zhekun Shi, Longlin Yu, Tianyu Xie, Cheng Zhang.
Preprint, arXiv:2410.15336, 2024
[Paper]

Hierarchical Semi-Implicit Variational Inference with Application to Diffusion Model Acceleration
Longlin Yu$^\ast$, Tianyu Xie$^\ast$, Yu Zhu$^\ast$, Tong Yang, Xiangyu Zhang, Cheng Zhang.
Advances in Neural Information Processing Systems (NeurIPS), 2023
[Paper] [Code]

ARTree: A Deep Autoregressive Model for Phylogenetic Inference
Tianyu Xie, Cheng Zhang.
Advances in Neural Information Processing Systems (NeurIPS, spotlight), 2023
[Paper] [Code]

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